Variant report

Variant	rs12591308
Chromosome Location	chr15:100227835-100227836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:100104749..100107658-chr15:100227633..100229523,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10468175	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11247112	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11247116	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs11631947	0.84[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap]
rs12324876	0.87[ASN][1000 genomes]
rs12438623	0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442313	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12913830	0.80[AMR][1000 genomes]
rs1991921	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs2012129	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs325405	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4564541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4965260	0.84[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap]
rs4965533	0.81[GIH][hapmap];0.80[AMR][1000 genomes]
rs4965534	0.81[AMR][1000 genomes]
rs62040141	0.89[ASN][1000 genomes]
rs62040142	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7162940	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs7172418	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs7173943	0.81[CHB][hapmap];0.83[MKK][hapmap]
rs7181542	0.84[ASW][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8029326	0.92[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8037206	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv904562	chr15:100214935-100237682	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12591308	MEF2A	cis	cerebellum	SCAN
rs12591308	LYSMD4	cis	parietal	SCAN
rs12591308	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100171200-100232800	Weak transcription	Esophagus	oesophagus
3	chr15:100171200-100248800	Weak transcription	Gastric	stomach
4	chr15:100172000-100230800	Weak transcription	Stomach Mucosa	stomach
5	chr15:100179200-100232600	Weak transcription	Colonic Mucosa	Colon
6	chr15:100181800-100232800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:100192000-100230400	Weak transcription	NHLF	lung
8	chr15:100193000-100229000	Weak transcription	Lung	lung
9	chr15:100199800-100232600	Weak transcription	Right Ventricle	heart
10	chr15:100209800-100232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:100211800-100232200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:100212800-100240000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:100213000-100232600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:100213400-100232600	Weak transcription	Pancreas	Pancrea
16	chr15:100213600-100243400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:100215800-100230800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:100216200-100229800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:100216200-100230200	Weak transcription	HMEC	breast
20	chr15:100216200-100232600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:100216200-100233000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:100216400-100229600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:100216800-100230200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:100216800-100230400	Weak transcription	Placenta	Placenta
25	chr15:100216800-100232200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:100217000-100232800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:100217400-100232600	Weak transcription	Fetal Intestine Small	intestine
28	chr15:100218000-100230400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:100218200-100232600	Weak transcription	Hela-S3	cervix
30	chr15:100218200-100232800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:100219400-100230200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:100219400-100248200	Weak transcription	Small Intestine	intestine
33	chr15:100219600-100229400	Weak transcription	Fetal Kidney	kidney
34	chr15:100219600-100248400	Weak transcription	Spleen	Spleen
35	chr15:100219800-100230400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:100219800-100230600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:100219800-100243600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr15:100220400-100232600	Weak transcription	Thymus	Thymus
39	chr15:100220400-100233000	Weak transcription	Right Atrium	heart
40	chr15:100221800-100229200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:100221800-100232000	Weak transcription	Psoas Muscle	Psoas
42	chr15:100222000-100232600	Weak transcription	Aorta	Aorta
43	chr15:100222800-100243600	Weak transcription	Brain Angular Gyrus	brain
44	chr15:100223000-100230400	Weak transcription	Osteobl	bone
45	chr15:100223400-100228600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:100223600-100230000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:100223600-100232600	Weak transcription	NHEK	skin
48	chr15:100223600-100232800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:100223600-100236600	Strong transcription	Fetal Lung	lung
50	chr15:100223600-100247400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links